Complement component 3 (C3) is a core component of the complement system, and directly participates in immune regulation and immune defense. Isoforms of C3 have been reported in several species of vertebrate, but invertebrates, and more specifically clams, have been less well studied. An isoform of C3, named ScC3-2, was identified in Sinonovacula constricta (Chinese razor clam). ScC3-2 included eight conserved regions, a thioester bond and two predicted junction sites (α-β and α-γ). The gene was expressed in the liver, gill, foot, hemolymph, mantle, gonad and siphon tissues. The gene was significantly upregulated in umbo larvae, suggesting that initial larval immunity may develop in umbo larvae. Moreover, the ScC3-2 mRNA expression patterns after challenge with Vibrio parahemolyticus and Micrococcus lysodeikticus exhibited an obvious upregulation at 8 h in the hemolymph and at 4 h in the liver, respectively. Furthermore, ScC3-2 showed effective membrane rupture of heterologous rabbit erythrocytes. The ScC3-2 protein was located on the surface of the cells during the process of hemolysis. After a comparative analysis, we suggest that the major structure and function of ScC3 and ScC3-2 are analogous. Our findings suggest that ScC3-2 plays an important immune function, and an intricate complement response may exist in S. constricta.